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- PDB-6p59: Crystal structure of SIVrcm Vif-CBFbeta-ELOB-ELOC complex -

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基本情報

登録情報
データベース: PDB / ID: 6p59
タイトルCrystal structure of SIVrcm Vif-CBFbeta-ELOB-ELOC complex
要素
  • Core-binding factor subunit beta
  • Elongin-B
  • Elongin-C
  • Virion infectivity factor
キーワードviral protein/immune system / Complex / Vif / A3G / VIRAL PROTEIN / viral protein-immune system complex
機能・相同性
機能・相同性情報


RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX2 regulates bone development / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / RUNX2 regulates chondrocyte maturation / negative regulation of CD4-positive, alpha-beta T cell differentiation / lymphocyte differentiation ...RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX2 regulates bone development / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / RUNX2 regulates chondrocyte maturation / negative regulation of CD4-positive, alpha-beta T cell differentiation / lymphocyte differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / RUNX2 regulates genes involved in cell migration / RUNX2 regulates genes involved in differentiation of myeloid cells / Transcriptional regulation by RUNX2 / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / myeloid cell differentiation / target-directed miRNA degradation / RUNX3 Regulates Immune Response and Cell Migration / elongin complex / VCB complex / definitive hemopoiesis / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of RUNX1 Expression and Activity / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / RUNX2 regulates osteoblast differentiation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RUNX3 regulates p14-ARF / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / cell maturation / RNA Polymerase II Pre-transcription Events / viral life cycle / transcription corepressor binding / transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / osteoblast differentiation / Transcriptional regulation of granulopoiesis / protein polyubiquitination / Regulation of RUNX2 expression and activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / Estrogen-dependent gene expression / sequence-specific DNA binding / host cell cytoplasm / transcription by RNA polymerase II / transcription coactivator activity / protein ubiquitination / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / host cell plasma membrane / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / plasma membrane / cytosol
類似検索 - 分子機能
Polyomavirus Enhancer Binding Protein 2; Chain: A; / Core binding factor, beta subunit / Retroviral Vif (Viral infectivity) protein / Retroviral Vif (Viral infectivity) protein / Core-binding factor, beta subunit / Core-binding factor, beta subunit superfamily / Core binding factor beta subunit / Elongin B / Elongin-C / Potassium Channel Kv1.1; Chain A ...Polyomavirus Enhancer Binding Protein 2; Chain: A; / Core binding factor, beta subunit / Retroviral Vif (Viral infectivity) protein / Retroviral Vif (Viral infectivity) protein / Core-binding factor, beta subunit / Core-binding factor, beta subunit superfamily / Core binding factor beta subunit / Elongin B / Elongin-C / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
Virion infectivity factor / Core-binding factor subunit beta / Elongin-C / Elongin-B
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Simian immunodeficiency virus (サル免疫不全ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.94221405643 Å
データ登録者Binning, J.M. / Chesarino, N.M. / Emerman, M. / Gross, J.D.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082250 米国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI120867 米国
引用ジャーナル: Cell Host Microbe / 年: 2019
タイトル: Structural Basis for a Species-Specific Determinant of an SIV Vif Protein toward Hominid APOBEC3G Antagonism.
著者: Binning, J.M. / Chesarino, N.M. / Emerman, M. / Gross, J.D.
履歴
登録2019年5月29日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年12月25日Provider: repository / タイプ: Initial release
改定 1.12023年10月11日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
C: Core-binding factor subunit beta
W: Elongin-B
Z: Elongin-C
F: Virion infectivity factor
A: Core-binding factor subunit beta
D: Elongin-B
E: Elongin-C
B: Virion infectivity factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)142,42913
ポリマ－141,9198
非ポリマー5105
水1267
1
C: Core-binding factor subunit beta
W: Elongin-B
Z: Elongin-C
F: Virion infectivity factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)71,1176
ポリマ－70,9604
非ポリマー1582
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10740 Å2
ΔGint-60 kcal/mol
Surface area27010 Å2
手法PISA
2
A: Core-binding factor subunit beta
D: Elongin-B
E: Elongin-C
B: Virion infectivity factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)71,3127
ポリマ－70,9604
非ポリマー3533
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10830 Å2
ΔGint-61 kcal/mol
Surface area27540 Å2
手法PISA
単位格子
Length a, b, c (Å)110.220, 112.489, 125.697
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22
13
23
14
24

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUMETMET(chain F and (resseq 3:5 or (resid 7 and (name...FD3 - 53 - 5
121ILEILEPROPRO(chain F and (resseq 3:5 or (resid 7 and (name...FD7 - 497 - 49
131GLYGLYGLUGLU(chain F and (resseq 3:5 or (resid 7 and (name...FD51 - 7951 - 79
141GLYGLYCYSCYS(chain F and (resseq 3:5 or (resid 7 and (name...FD81 - 9781 - 97
151PROPROGLUGLU(chain F and (resseq 3:5 or (resid 7 and (name...FD99 - 13499 - 134
161VALVALLYSLYS(chain F and (resseq 3:5 or (resid 7 and (name...FD136 - 166136 - 166
171GLNGLNSERSER(chain F and (resseq 3:5 or (resid 7 and (name...FD200 - 205200 - 205
181VALVALTHRTHR(chain F and (resseq 3:5 or (resid 7 and (name...FD207 - 218207 - 218
211GLUGLUMETMET(chain B and (resseq 3:5 or (resid 7 and (name...BH3 - 53 - 5
221ILEILEPROPRO(chain B and (resseq 3:5 or (resid 7 and (name...BH7 - 497 - 49
231GLYGLYGLUGLU(chain B and (resseq 3:5 or (resid 7 and (name...BH51 - 7951 - 79
241GLYGLYCYSCYS(chain B and (resseq 3:5 or (resid 7 and (name...BH81 - 9781 - 97
251PROPROGLUGLU(chain B and (resseq 3:5 or (resid 7 and (name...BH99 - 13499 - 134
261VALVALLYSLYS(chain B and (resseq 3:5 or (resid 7 and (name...BH136 - 166136 - 166
271GLNGLNSERSER(chain B and (resseq 3:5 or (resid 7 and (name...BH200 - 205200 - 205
281VALVALTHRTHR(chain B and (resseq 3:5 or (resid 7 and (name...BH207 - 218207 - 218
112TYRTYRLEULEU(chain Z and (resseq 18:51 or (resid 52 and (name...ZC18 - 11018 - 110
212TYRTYRLEULEU(chain E and (resseq 18:51 or (resid 52 and (name...EG18 - 11018 - 110
113PROPROASNASN(chain A and (resseq 6:11 or (resid 12 and (name...AE6 - 146 - 14
123GLUGLUSERSER(chain A and (resseq 6:11 or (resid 12 and (name...AE16 - 2216 - 22
133GLUGLUSERSER(chain A and (resseq 6:11 or (resid 12 and (name...AE24 - 7224 - 72
143GLNGLNLEULEU(chain A and (resseq 6:11 or (resid 12 and (name...AE74 - 8874 - 88
153ARGARGGLNGLN(chain A and (resseq 6:11 or (resid 12 and (name...AE90 - 13390 - 133
163ALAALAGLNGLN(chain A and (resseq 6:11 or (resid 12 and (name...AE137 - 140137 - 140
173ALAALAARGARG(chain A and (resseq 6:11 or (resid 12 and (name...AE142 - 148142 - 148
183THRTHRASPASP(chain A and (resseq 6:11 or (resid 12 and (name...AE150 - 157150 - 157
193SERSERSERSER(chain A and (resseq 6:11 or (resid 12 and (name...AE159159
213PROPROASNASN(chain C and (resseq 6:11 or (resid 12 and (name...CA6 - 146 - 14
223GLUGLUSERSER(chain C and (resseq 6:11 or (resid 12 and (name...CA16 - 2216 - 22
233GLUGLUSERSER(chain C and (resseq 6:11 or (resid 12 and (name...CA24 - 7224 - 72
243GLNGLNLEULEU(chain C and (resseq 6:11 or (resid 12 and (name...CA74 - 8874 - 88
253ARGARGGLNGLN(chain C and (resseq 6:11 or (resid 12 and (name...CA90 - 13390 - 133
263ALAALAGLNGLN(chain C and (resseq 6:11 or (resid 12 and (name...CA137 - 140137 - 140
273ALAALAARGARG(chain C and (resseq 6:11 or (resid 12 and (name...CA142 - 148142 - 148
283THRTHRASPASP(chain C and (resseq 6:11 or (resid 12 and (name...CA150 - 157150 - 157
293SERSERSERSER(chain C and (resseq 6:11 or (resid 12 and (name...CA159159
114METMETPHEPHE(chain W and (resseq 1 or (resid 2 and (name...WB1 - 251 - 25
124LEULEUPHEPHE(chain W and (resseq 1 or (resid 2 and (name...WB27 - 7927 - 79
134THRTHRTHRTHR(chain W and (resseq 1 or (resid 2 and (name...WB8484
144GLUGLUPROPRO(chain W and (resseq 1 or (resid 2 and (name...WB86 - 9786 - 97
254METMETPHEPHE(chain D and (resseq 1 or (resid 2 and (name...DF1 - 251 - 25
264LEULEUPHEPHE(chain D and (resseq 1 or (resid 2 and (name...DF27 - 7927 - 79
274THRTHRTHRTHR(chain D and (resseq 1 or (resid 2 and (name...DF8484
284GLUGLUPROPRO(chain D and (resseq 1 or (resid 2 and (name...DF86 - 9786 - 97

NCSアンサンブル:
ID
1
2
3
4

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要素

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タンパク質 , 4種, 8分子 CAWDZEFB

#1: タンパク質 Core-binding factor subunit beta / CBF-beta / Polyomavirus enhancer-binding protein 2 beta subunit / PEBP2-beta / SL3-3 enhancer ...CBF-beta / Polyomavirus enhancer-binding protein 2 beta subunit / PEBP2-beta / SL3-3 enhancer factor 1 subunit beta / SL3/AKV core-binding factor beta subunit


分子量: 19701.965 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CBFB / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q13951
#2: タンパク質 Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


分子量: 13147.781 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ELOB, TCEB2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q15370
#3: タンパク質 Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


分子量: 12485.135 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ELOC, TCEB1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q15369
#4: タンパク質 Virion infectivity factor


分子量: 25624.660 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Simian immunodeficiency virus (サル免疫不全ウイルス)
遺伝子: vif / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: E1ANT9

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非ポリマー , 4種, 12分子

#5: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Zn
#6: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H8O3
#7: 化合物 ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / 2-モルホリノエタンスルホン酸


分子量: 195.237 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C6H13NO4S / コメント: pH緩衝剤*YM
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 7 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.75 Å3/Da / 溶媒含有率: 55.2 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: MES (pH 6), PEG 6000, Dichloromethane

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: ALS / ビームライン: 8.3.1 / 波長: 1.11583 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2015年9月3日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1.11583 Å / 相対比: 1
反射解像度: 2.94→49.12 Å / Num. obs: 33445 / % possible obs: 98.8 % / 冗長度: 7.2 % / Biso Wilson estimate: 85.66762804 Å2 / Net I/σ(I): 12.27
反射 シェル解像度: 2.94→3.047 Å / Num. unique obs: 3146

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解析

ソフトウェア
名称分類
PHENIX精密化
Cootモデル構築
Blu-Iceデータ収集
HKL-2000データ削減
HKL-2000データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4N9F

4n9f


解像度: 2.94221405643→49.116978298 Å / SU ML: 0.433819171318 / 交差検証法: FREE R-VALUE / σ(F): 1.32565720389 / 位相誤差: 32.7423150686
Rfactor反射数%反射
Rfree0.268464117183 1679 5.02273543137 %
Rwork0.234530316465 --
obs0.236271019504 33428 98.7679125425 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 98.7828845439 Å2
精密化ステップサイクル: LAST / 解像度: 2.94221405643→49.116978298 Å
タンパク質核酸リガンド溶媒全体
原子数8892 0 26 7 8925
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.005840464889869138
X-RAY DIFFRACTIONf_angle_d0.86175809537812338
X-RAY DIFFRACTIONf_chiral_restr0.04964108481981288
X-RAY DIFFRACTIONf_plane_restr0.005860797357711596
X-RAY DIFFRACTIONf_dihedral_angle_d17.96629831755480
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9422-3.02880.4385743046911260.3747675982942460X-RAY DIFFRACTION92.7879440258
3.0288-3.12650.3631239383821480.3387874368982632X-RAY DIFFRACTION99.9640417116
3.1265-3.23820.3358978059371360.3090544365972639X-RAY DIFFRACTION99.9639769452
3.2382-3.36790.3350985912821380.3069548008422628X-RAY DIFFRACTION99.9277456647
3.3679-3.52110.3150601217811380.3061008463642664X-RAY DIFFRACTION99.9643239386
3.5211-3.70670.4357441305261370.3631452166052540X-RAY DIFFRACTION96.3642908567
3.7067-3.93880.3284588238561410.2789687304522586X-RAY DIFFRACTION96.8738898757
3.9388-4.24280.232859697351370.2192178816442665X-RAY DIFFRACTION99.9643239386
4.2428-4.66950.2007111057021460.1788776754222683X-RAY DIFFRACTION99.8940677966
4.6695-5.34440.2203508361991430.1848759614742674X-RAY DIFFRACTION99.9645138396
5.3444-6.73070.2827695723211430.2127165615162740X-RAY DIFFRACTION99.9653259362
6.7307-49.12380.2030164293751460.1861292660582838X-RAY DIFFRACTION99.4666666667
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.2672155973560.569191207568-0.1268988883340.494955833465-0.9920517293751.55448642286-0.29029447438-0.4623670269810.286207377573-0.503978561228-0.3481064426610.5734948753830.0705569423693-0.4955386517253.3681867585E-50.6965198450750.1666188986710.08617316666530.82850004189-0.1004283216450.99321067574955.77326535555.570858868823.742973347
20.257711166076-0.0231832320760.1521109263240.422509851339-0.5172115181130.359311351903-0.126599276123-0.291714996830.168724033575-0.17496812546-0.232023071877-0.420466424510.731478000743-0.0352540281169-9.1931956663E-50.459286546970.09729846104720.02551868466790.9620800148770.05122023046630.65164222170163.4185014515-9.734555877525.444087862
3-0.05259356559150.09995108268530.004756772373941.348143492440.8115889915980.456820738256-0.132873259853-0.8022267215320.8941160732550.162262909461-0.568393334513-1.13902231338-0.011396740023-0.766648200719-0.007984752111320.7976548948590.0291035347192-0.1827967512421.3957508117-0.2635610458581.0648239011171.3129017586-0.61308473447329.3504071933
40.1705257484610.5009999024630.5122130859760.6563799645370.2916581463921.16297681045-1.23489380046-1.910057009891.181207904361.212071268681.118139089770.460447664390.302545682660.00343004508283-0.07437367386540.147971694437-0.353566991088-0.5200384924151.11166634579-0.6342149288571.052572703460.58719433383.1250070359930.2996419366
50.566516907528-0.092509071029-0.465325208897-0.06665754845530.05819908976260.2965486484351.24358255441-2.269249884490.197782314559-0.0389811493261-1.117097772380.471369384856-0.4364928371280.4728820093120.001050265649631.33749459101-0.11221143621-0.3795308689811.207490265380.05446801981.3700198290169.092818266920.121047724418.2924360259
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220.359757298505-0.1287024700210.5301910120650.181414238948-0.2452968328740.643558843554-0.0366242538926-0.469363796294-0.2886769181831.375633375850.3539652994810.0411506732773-0.957102955976-0.2049313072548.39781678236E-50.949939825519-0.03097319768040.008646780123260.9121728328090.09240285904550.46574559976766.27902302831.70524119848-32.4812069236
230.23840108867-0.652332346396-0.02272791873053.02400371194-0.9299927569920.5876052379120.698570131306-1.980832967980.8508734932481.48799649134-1.43938746491-1.005561512240.0172203058787-0.119866069555-0.06844521736230.807301811847-0.282153024399-0.3287042081591.378911824190.08359628829580.94967299393377.10269940918.2782723151-39.3175327862
241.23972069093-1.291593215790.6780841836370.444938273917-0.343284974180.4090257669690.102975010907-0.157873936520.6520212197680.548070309557-0.1237098800580.153944714991-0.525044559758-0.523188038179-0.1226936451010.5060959913890.030962660422-0.03681457766890.3623729116750.08739897314960.64043205550966.426534361223.6353514781-64.959201209
250.09323872047270.1894495315170.002282700618180.7127225092050.1563446252480.15612271084-1.00871429908-0.678753740916-0.207912144335-0.271076020595-0.1176803854030.425490949240.2786324606040.0197020657612-0.1426502343060.672995318580.09476124296640.250898166890.8147384772160.1465110147820.47584102645436.274478875828.638239443-46.5912923845
260.7159951312670.2906606267590.1486082486720.1564439606770.1485712304520.464095740986-0.388961286388-0.3701037002530.5925024459120.443335035063-0.175321544987-0.1235973890170.315390180848-0.281936082502-0.1398044435070.6744509936230.05766244272540.07480346628260.7007368528910.02329318544680.50908276136436.173093216131.2091782247-45.1823981405
270.354059953750.323572333404-0.1049408210560.209777466278-0.0556260787450.1893826307530.849902775328-0.6794096299280.1966794167021.51785187509-0.5104364457170.255980831695-0.894707780850.3208479850250.004325586215790.748688572041-0.09833188612080.07279184911890.797256426415-0.07509531154250.47066615506634.144518467136.9228923693-38.358687954
281.5784026343-0.171773058793-1.222508558560.2871465300930.4120630048380.980963248805-0.353080626469-0.387560053554-0.05721468232110.4983063997250.1620151029770.589843430525-0.14414775375-0.2826792914664.9340888108E-50.9915116708350.01217254053430.1003809437120.690054955920.09365402765610.67924312306226.632721045631.110013542-39.679438015
291.423291055971.04080415518-0.07727326303770.6909501081260.07387340486611.43120445317-0.0908637424845-0.0076475086348-0.5707507529420.46716436443-0.4235750276640.6660291951680.474285216612-0.636299015283-0.01978696683640.6257042696990.006889680609470.07991286913010.617587782315-0.03708247629240.55842114411128.644451305531.0466133349-48.0954855951
300.0454129497885-0.0596210808103-0.03292450811130.08926859120080.04220891181480.09200167480830.517357626977-0.73832311302-0.73635662205-0.3676716387660.56451937291-0.5275461407150.105207686523-0.3189878574740.0007184232132690.7593727534270.082084121637-0.334327582580.677530958917-0.3527815805711.0587527057232.481428184327.7557776505-70.7201957176
310.991078843771-0.309117077826-1.081198821491.93641670270.04599258389160.8864893043250.0860354358935-0.2491503049710.2205140634730.05270148127270.0228130132545-0.03062013452630.09015465518650.2201148458580.000189312758180.512622753773-0.0358173845132-0.02372077069140.554445953982-0.0001919677852910.36762501677947.003963091141.2071487791-54.8291140157
320.491610569813-0.4232614307580.1523859188410.433913004945-0.2113002916980.1119886000520.2316555314140.4124941347371.300248799630.8322295493820.31531028210.703640294334-0.6946384359350.08181351168160.0117007607510.881829354591-0.05591324030280.0358543918490.532959946204-0.05424631348990.64943364493644.938122419744.6282375479-59.1627340218
330.432929142369-0.402179504455-0.2673745306660.3554759560620.4909178011460.514868026335-0.147505017896-0.165969984225-0.4139807097320.1522522003120.0187725840935-0.2543468524850.8438362128830.08051506373720.0003229712574670.5319251876770.0873323772651-0.108971087710.6580551931650.004635946969540.49124598812644.359369677128.773615658-56.7189196409
340.449443522825-0.0230066609043-0.4692504437710.00132675092839-0.03541071534210.4493352547940.0386466159654-0.706852653333-1.02808136715-0.2989096310221.174399106220.4715247716540.104696597804-0.6038551093270.0173027300760.6657594655280.0567274139666-0.08234660436860.4830365872320.1697755775830.67031234942249.564884098218.7219533207-54.0308614896
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391.89270128970.311588372156-1.410608187662.67119166622-0.3702152435361.07387693857-0.5476698181430.3643197862780.940256366713-0.7959612831120.8749431835831.148385023980.8176765903790.6760531045920.298575171131.94425629867-0.291429595392-0.2453560565720.7128624245610.1031966595190.83409762091340.72253591819.2307848666-81.5131840699
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 6 through 36 )
2X-RAY DIFFRACTION2chain 'C' and (resid 37 through 73 )
3X-RAY DIFFRACTION3chain 'C' and (resid 74 through 93 )
4X-RAY DIFFRACTION4chain 'C' and (resid 94 through 127 )
5X-RAY DIFFRACTION5chain 'C' and (resid 128 through 148 )
6X-RAY DIFFRACTION6chain 'C' and (resid 149 through 160 )
7X-RAY DIFFRACTION7chain 'W' and (resid 1 through 23 )
8X-RAY DIFFRACTION8chain 'W' and (resid 24 through 46 )
9X-RAY DIFFRACTION9chain 'W' and (resid 47 through 60 )
10X-RAY DIFFRACTION10chain 'W' and (resid 61 through 77 )
11X-RAY DIFFRACTION11chain 'W' and (resid 78 through 92 )
12X-RAY DIFFRACTION12chain 'W' and (resid 93 through 98 )
13X-RAY DIFFRACTION13chain 'Z' and (resid 17 through 38 )
14X-RAY DIFFRACTION14chain 'Z' and (resid 39 through 58 )
15X-RAY DIFFRACTION15chain 'Z' and (resid 59 through 82 )
16X-RAY DIFFRACTION16chain 'Z' and (resid 83 through 112 )
17X-RAY DIFFRACTION17chain 'F' and (resid 3 through 106 )
18X-RAY DIFFRACTION18chain 'F' and (resid 107 through 220 )
19X-RAY DIFFRACTION19chain 'A' and (resid 5 through 36 )
20X-RAY DIFFRACTION20chain 'A' and (resid 37 through 73 )
21X-RAY DIFFRACTION21chain 'A' and (resid 74 through 83 )
22X-RAY DIFFRACTION22chain 'A' and (resid 84 through 127 )
23X-RAY DIFFRACTION23chain 'A' and (resid 128 through 138 )
24X-RAY DIFFRACTION24chain 'A' and (resid 139 through 161 )
25X-RAY DIFFRACTION25chain 'D' and (resid 1 through 9 )
26X-RAY DIFFRACTION26chain 'D' and (resid 10 through 23 )
27X-RAY DIFFRACTION27chain 'D' and (resid 24 through 35 )
28X-RAY DIFFRACTION28chain 'D' and (resid 36 through 60 )
29X-RAY DIFFRACTION29chain 'D' and (resid 61 through 93 )
30X-RAY DIFFRACTION30chain 'D' and (resid 94 through 98 )
31X-RAY DIFFRACTION31chain 'E' and (resid 17 through 53 )
32X-RAY DIFFRACTION32chain 'E' and (resid 54 through 66 )
33X-RAY DIFFRACTION33chain 'E' and (resid 67 through 82 )
34X-RAY DIFFRACTION34chain 'E' and (resid 83 through 96 )
35X-RAY DIFFRACTION35chain 'E' and (resid 97 through 112 )
36X-RAY DIFFRACTION36chain 'B' and (resid 3 through 53 )
37X-RAY DIFFRACTION37chain 'B' and (resid 54 through 106 )
38X-RAY DIFFRACTION38chain 'B' and (resid 107 through 164 )
39X-RAY DIFFRACTION39chain 'B' and (resid 165 through 174 )
40X-RAY DIFFRACTION40chain 'B' and (resid 175 through 220 )

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

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